ADDA: a domain database with global coverage

ADDA: a domain database with global coverage
D188–D191 Nucleic Acids Research, 2005, Vol. 33, Database issue
doi:10.1093/nar/gki096
ADDA: a domain database with global coverage of the
protein universe
Andreas Heger1,*, Christopher Andrew Wilton1, Ashwin Sivakumar1 and Liisa Holm1,2
1
Institute of Biotechnology and 2Department of Genetics, University of Helsinki, 00014 Helsinki, Finland
Received August 16, 2004; Revised and Accepted October 13, 2004
ABSTRACT
INTRODUCTION
The past and present periods of large-scale genome
sequencing have brought an enormous wealth of protein
sequences that makes managing, navigating and mining the
data an area of research in its own right.
Protein evolution suggests domains as a convenient unit
of classification. Mutations, insertions and deletions create
sequence diversity inside a domain family. On a higher level,
recombination events combine domains in different architectures to give the single- or multi-domain proteins we observe.
Various invaluable tools exist to reduce the diversity of
proteins into a reduced set of protein domain families.
Semi-automated methods such as Pfam (1), PROSITE (2)
or SMART (3) extrapolate the information gained from
known members of protein domain families by matching
sequences to libraries of hidden Markov models (HMMs),
profiles or patterns. Integrative projects such as InterPro (4)
combine various primary sources to yield a summary view on
protein sequences. Fully automated methods such as ProDom
(5) or DOMO (6) apply algorithms to achieve a classification
based on first principles.
DATABASE CONTENTS
The database contains more than 1.5 million sequences from
UniProt/Swiss-Prot, UniProt/TrEMBL (8), Ensembl (9), NCBI
genomes (10) and other sources of protein sequences. The
clustering yields 2.7 million domains, which are grouped
into 123 000 families. Of these, 40 000 families have more
than five members. The database is built in an entirely
automated fashion and is updated regularly.
DOMAIN AND DOMAIN FAMILY DEFINITION
The domain and domain family definitions result from an
automated clustering procedure applied to the set of all protein
*To whom correspondence should be addressed. Tel: +358 9 191 59115; Fax: +358 9 191 59366; Email: [email protected]
Correspondence may be addressed to Liisa Holm. Email: [email protected]
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We used the Automatic Domain Decomposition
Algorithm (ADDA) to generate a database of protein
domain families with complete coverage of all protein
sequences. Sequences are split into domains and
domains are grouped into protein domain families
in a completely automated process. The current database contains domains for more than 1.5 million
sequences in more than 40 000 domain families. In
particular, there are 3828 novel domain families that
do not overlap with the curated domain databases
Pfam, SCOP and InterPro. The data are freely
available for downloading and querying via a web
interface (http://ekhidna.biocenter.helsinki.fi:9801/
sqgraph/pairsdb).
Previously, we have introduced the Automatic Domain
Decomposition Algorithm (ADDA) (7), a method for clustering
very large sets of protein sequences. ADDA first splits sequences
into domains and then organizes these domains into protein
domain families. The classification is constructed in an entirely automated fashion from first principles and thus is not biased
by human curation, but only limited by the applied algorithms.
We have applied ADDA to the set of all known protein
sequences that are available in the major public databases.
Using all sequences for clustering has the advantage of drawing the boundaries between protein domain families in a globally consistent manner. This is in contrast to scanning methods
such as Pfam and SMART, where novel or hypothetical
sequences are scanned against a library of HMMs or profiles.
Matches at the borderline of significance can be due to a newly
discovered remote relative or to spurious similarity. In such
events, domain families have to be assigned case by case.
Here, we describe a database with a web interface that
allows scientists to download and browse the results. The web
interface lets a scientist explore the context of a protein
sequence in the protein universe: its immediate neighbours
as determined by pre-computed sequence similarity searches,
and its remote homologues as determined by its domain composition. Alternatively, a scientist can browse the domain
families to hunt for domain families of interest.
Nucleic Acids Research, 2005, Vol. 33, Database issue
sequences in the major public databases. The process starts by
removing sequences with >40% sequence identity to any other
sequence from the input set (11). The remaining representative
sequences are then aligned in an all-versus-all manner using
the BLAST (12) program.
Representative sequences are split into domains by the
ADDA algorithm. Domains are defined so that a minimum
number of alignments are intersected by domain boundaries
and these alignments cover domains as much as possible.
After splitting protein sequences, the resultant domains are
grouped into families of related sequences by a single-linkage
clustering algorithm. Domains joined by alignments are
grouped into a family if their domain boundaries are consistent. In addition, domains are compared using sensitive profile–
profile comparison. The merging process stops when the
sequence similarity between domains drops below a threshold.
Finally, domain boundaries are mapped from the representative sequences onto all sequences in the database.
Quality control monitors two aspects of the clustering by
comparing ADDA domains to curated databases of domain
families like Pfam and SCOP (13). The correspondence of
domain boundaries is checked by computing the relative overlap between ADDA and reference domains. ADDA tends to
split conservatively; ADDA domains are, on average, larger
than reference domains.
The correspondence of domain families is measured by
matching each ADDA family to the best matching reference
family and counting the relative frequency of other reference
families in the ADDA family (selectivity) and the relative
frequency of reference domains assigned to different ADDA
families (sensitivity). On average, an ADDA domain family
unifies 93% of the members of a Pfam family while containing
only 5% contamination.
Charts and summary statistics are available on the web
server.
ANNOTATING DOMAIN FAMILIES
In multi-domain proteins, domains of different protein
families co-occur. Based on the observed architecture of
protein sequences, domain families can be divided into two
groups: mobile modules and associated families. Mobile
modules are promiscuous and recombine with several other
domain families. Associated families either always occur in
single-domain proteins or are always associated with the same
domain family. In the present release, there are 9252 mobile
modules and 49 455 associated families (Figure 1A). While
the latter tend to be specific to a single kingdom (Archaea,
Bacteria and Eukaryota), mobile modules have a larger
taxonomic range (Figure 1B).
A domain family is declared to be structurally covered if
one of its domains can be mapped onto a structure in the PDB
database of protein structures (14). For each ADDA domain,
we register the sequence overlap with domains from curated
domain databases (Pfam, SCOP and InterPro). An ADDA
domain family is classified as novel if <5% of its domains
overlap with domains from the curated domain databases.
ADDA contains 3828 novel mobile modules that are
not known to curated domain databases and for which there
is no structural information available (Figure 1C). Novel
domain families tend to have fewer members (<200) than
well-known domain families. The number of novel domains
in associated families is even larger comprising 40 505 domain
families.
DATABASE ACCESS AND INTERFACE
The complete protein domain classification can be downloaded
from http://ekhidna.biocenter.helsinki.fi:8080/downloads/
adda. A web interface is available for browsing and querying
at http://ekhidna.biocenter.helsinki.fi:9801/sqgraph/pairsdb.
The interface allows the user to query for protein sequences
by identifier, accession number or sequence similarity. The
sequence view shows the decomposition of a protein sequence
into domains. Links allow the user to browse similar sequences
in the direct neighbourhood of a query sequence (multiple
alignments pre-computed using BLAST and PSI-BLAST) and
to switch to the domain families to get all related sequences
beyond the immediate neighbourhood.
Domain families of interest can be retrieved by custom
queries. Attributes available for querying are the size of the
family, its taxonomic spread, its structural coverage, the
number of associated domains (querying for mobile modules),
the overlap with other domain classifications (querying for
novel domain families) and others. The domain family view
includes a summary overview over the protein family and links
to other domain classifications. The sequences of all domains
in a domain family can be downloaded for local analysis.
If structures are known in the family, the domain boundaries
are mapped onto the structures for visualization with
RASMOL (15).
In the browsing section, the user finds links to precompiled
domain sets of interest, e.g. all exclusively eukaryotic mobile
domains or a list of domain families without known structures
(structural genomics targets). In addition, a genome browser
allows access to all or a selection of domain families occurring
in a genome.
The web server contains outgoing links to external databases for sequences and domains. For example, ADDA is
linked to by the Dali domain database (16) and vice versa.
EXAMPLE
Links and attributes can be queried in numerous ways. One
application of the database interface is to hunt for novel
domain families. For example, typing ‘sapiens’ into the
genome browser lists 28 791 domain families in human protein
sequences. The result set can be restricted to exclude domain
families that have domains from Archaea or Bacteria and/or
are not novel and not a mobile module giving 7933 domain
families. Modifying the query to include only domains with
more than 20 members produces 108 novel domain families that occur in human protein sequences, are specific to
eukaryotes and have at least 20 members.
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QUALITY CONTROL
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Nucleic Acids Research, 2005, Vol. 33, Database issue
WORK IN PROGRESS
Our aim is to push the functional annotation of proteins as far
as possible using only automated methods. Defining domain
families is the first step. We are currently testing methods to
split domain families into groups of orthologous proteins and
automated methods to define functionally important residues
in a family.
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Figure 1. Overview of domain families in ADDA. The number of families is given in the last row of each category label. (A) Mobile modules, domain families that
co-occur with a variety of different domain families, constitute only a fraction of all domain families. Many domains only occur in single-domain proteins or are
always associated with the same domain family (associated families). The majority of domain families contain only a single representative sequence on the 40%
similarity level (singletons). (B) Taxonomic distribution of domain families over the three superkingdoms (Archaea, Bacteria and Eukaryota). Left: only associated
domain families excluding singletons. Right: only mobile modules. Mobile modules tend to be more widely distributed than associated domains. (C) Annotation of
domain families. Left: only associated domain families excluding singletons. Right: only mobile modules. Novel domain families do not overlap with domain
families from Pfam, SCOP and InterPro. Mobile modules are well known to curated domain databases, but there are many novel domain families left to be explored.
Nucleic Acids Research, 2005, Vol. 33, Database issue
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